The U.S. relationship with Pakistan is in crisis after last weekend's deadly border incident in which NATO troops killed 24 Pakistani soldiers along the Afghan border. The Pakistanis have cut off a key NATO supply line to Afghanistan, and they refused to take part in an upcoming conference on Afghanistan, which begins tomorrow.

They're demanding a full apology from the United States, something that American officials have been unwilling to give, at least until a military investigation establishes what went wrong.

NPR's Corey Flintoff is on the line with us from Islamabad.

Corey, to begin, tell us what's the status of that investigation.

COREY FLINTOFF, BYLINE: Pakistan's military has refused to even cooperate with the investigation. So all we have to go on is a series of public statements and leaks, basically. NATO officials say there were mistakes made on both sides. Each side apparently thought it was being fired upon by the Taliban. Then communications broke down and the NATO side called in airstrikes on what turned out to be a Pakistani position.

CORNISH: But these cross-border incidents have happened before. There was one in which Pakistani troops were accidently killed by a NATO strike in September of last year. And those problems have been quietly worked out in the past. So, Pakistan's reaction to this incident has been much stronger and I'm wondering what's different this time.

FLINTOFF: This time, the death toll was much higher - 24 soldiers dead. But I also talked with some analysts in the city of Lahore who say this is really a reaction to a lot of things that made Pakistan angry over the past year. You know, there was the Raymond Davis affair; that's when a CIA contractor killed two Pakistanis men in Lahore in January.

Then in May, there was the killing of Osama bin Laden, and that was a real blow to the prestige of the Pakistani military and the intelligence service, the ISI, because it showed that Pakistan couldn't defend its own airspace. And this latest incident was similar because it seemed to show that the Pakistani military couldn't even defend its own soldiers.

CORNISH: And as we mentioned, one reaction was to cut off a key NATO supply route to Afghanistan. How serious is that move?

FLINTOFF: A lot supplies for NATO, especially water and fuel, travel up that road from Karachi to the Afghan border. It's supposedly about 50 percent of the overall needs for the war. NATO officials say that if that closure were to last for, say, 60 days, it could really affect the war effort. Analysts say that's a very strong bargaining chip. But there is the danger that the Pakistani military will overplay its hand.

This is Rashed Rahman. He is the editor of an influential newspaper called the Daily Times

RASHED RAHMAN: I think our military and ISI - which has always had the Americans and NATO over a barrel on this question of logistics and on this question of access, and so on, and on intelligence and, you know, other cooperation - they feel they have them over a bigger barrel now.

FLINTOFF: That he says could lead the military to use this crisis as a pretext for getting a stronger hand in their relationship with the U.S., and demanding a more influential role in Afghanistan.

CORNISH: And so, given all of these tensions, what are the prospects for actually resolving this particular crisis?

FLINTOFF: The analysts think the issue has to be resolved because each side needs the other. This is Hasan Askari-Rizvi, a national security analyst. He pointed out to me that Pakistan has been reaching out to other countries in a way that it hasn't done before. Here's what he said:

DR. HASAN ASKARI-RIZVI: They are contacting the countries that have good relations with the United States. So that they can also - on the one hand you show pressure and express your displeasure and anger. On the other hand, you don't close the door for dialogue.

FLINTOFF: Now, since Pakistan has refused to participate in the conference on Afghanistan that starts tomorrow in Bonn, it's not clear when that dialogue would get fully underway.